Hello,
I run QIIME2 on terminal. Now I wanted to run PICRUSt2 as a qimme2 plugin but a bit confused as to how to move forward with it. I have used the following command to get PICRUSt2 but I guess this doesn't integrate PICRUSt as QIIME2 plugin. Please guide me with steps on how to proceed.
conda env create -f picrust2-env.yaml
source activate picrust2
pip install --no-deps --editable .
Which version of QIIME 2 are you running this on? I think the most recent version that is available is for 2021.11. Have you tried the manual install instructions?
I am using QIMME2 2022.2 and this is the latest version. Which version of PICRUSt is compatible with this updated QIIME2 ?
It looks like the picrust2 developers do not have a version for 2022.2 yet, so you will want to create a QIIME2 2021.11 environment, follow this link and be sure to click the red "show me the content on this page" button. Then activate that environment and install picrust and the 2021.11 picrust plugin version from the manual install page.
We are working on making the process for community developers to keep their plugins up-to-date a bit more hands off, so hopefully this sort of issue will be less prevalent in the future. Let me know if you run into any issues!
Thank you, I will follow the instructions you shared and let you know if it worked.
I also wanted to ask, is there a way to run PICRUSt2 independently without QIIME2
If yes, then can you help me with the instructions for the same?
Thank you!
You can run PICRUSt2 on its own, you will loose provenance tracking and other features found in QIIME 2, as well as having to perform manual imports to bring your data back into the QIIME 2 ecosystem, but q2-picrust2 is really just a wrapper for PICRUSt2. I do not have any experience running it by it self, but you will have already installed it on your system as part of the manual install. There is a wiki with more instructions on using it directly on the picrust Github page.
Thank you for the information. I wanted to ask if I QIIME2 2021.11 environment to add PICRUSt2 plug in, then can I use the output files generated by QIMME 2022.2? I am asking because I already ran QIMME 2022.2 version for a project and now I need to process with PICRUSt2 for the same project?
You should have no problem doing this!
Thank you so much for all your prompt help. One last question, is there a command line available to run q2-picrust2 for obtaining KEGG, EC and pathway output similar to the ones available for running QIIME2?
I am using q2 picrust2 Tutorial - picrust/picrust2 GitHub Wiki to run PICRUSt2 Hopefully this is the right one
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